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Searching BioCyc

Searching BioCyc. Ron Caspi. Help is One Click Away!. The Web Account System. The Web Account System. Creating a web account enables you to: Save Object Groups Define page formatting preferences Define Overview layout preferences Save organism groups for comparative analysis.

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Searching BioCyc

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  1. Searching BioCyc Ron Caspi

  2. Help is One Click Away!

  3. The Web Account System

  4. The Web Account System Creating a web account enables you to: • Save Object Groups • Define page formatting preferences • Define Overview layout preferences • Save organism groups for comparative analysis

  5. Save Organism Groups with Web Accounts • Note the My Lists tab on the multi-organism selector for comparative analyses. • When you perform comparative analyses, you can easily save groups of organisms for re-using at a later time.

  6. Define a Favorite Database with Web Accounts If you create a web account, you can define a favorite database that will be opened by default when you login

  7. Searching

  8. Why the Need for Dedicated Search Tools Search BioCyc for “L-arginine” 2080 results Need to have specific tools for finding exactly what we search for.

  9. BioCyc Searches • Multiple searches available for finding information in different ways • The easiest searches to use are fairly coarse • Start by selecting database to search • Simplest search: Quick Search • At upper right of most pages

  10. Selecting the Database You can only search one database at a time*! * With the exception of Google searches • Click on word “change” under Search menu or under Quick Search button • In resulting selector, choose a PGDB • Start typing a word in organism name • Click on letter to navigate to organisms starting with that letter • Click a frequently used PGDB • Select by Taxonomy • All subsequent searches will apply to that database

  11. The Quick Search Box • What can you type here: • Gene names (dnaA ) • Compound name (L-lysine) • Pathway name (peptidoglycan biosynthesis) • Reaction name (lysine decarboxylase) • Protein name (peptidase) • EC number (1.3.1.26) • Organism name (Escherichia coli) • Frame ID (CPLX-8024) • GO term (0006086) • Links to other databases (O33998) • An exact term using the format (Peptidase D search:exact) • Limited term (hydrogen type:compound) • What doesn’t work: • Exact text using the Google format (“peptidase D”)

  12. Quick Search Results Results are divided into multiple categories

  13. Examples of searches performed by users of the BioCyc website: SuccessfulUnsuccessful Ascorbate pheV EC 3.4.17.5 Transmembrane helix 6 Sigma factor 3.4.24.B11 Polysulfide reductase ABC cobalt transporter Entner-Doudoroff pathway affinity of DnaA Cyanobacteria DnaA A simple auto-correction mechanism tries to correct typos. For example, searching for “sacrosine” will find “sarcosine”.

  14. Quick Gene Search • Useful when only interested in genes. • For example, compare the results when searching for “dnaA” by using the Quick Search and Gene Search buttons.

  15. The Search Menu • Search Menu • Object-specific searches • Advanced search • Ontologies search • Google search • BLAST search • Search of full-text articles (EcoCyc only)

  16. Google This Site The BioCyc site is indexed by Google You can launch a Google text search from: 1. Search → Google This Site 2. The alternative searches box that appears on Quick Search results pages

  17. Object-Specific Searches • The first four items in the search menu provide a medium-level search interface against single types of objects • Use of filtering Click on triangles at the left to expand or hide filters Note that if a filter is hidden it will not be used in a search

  18. Compound Search • List All buttons – quick way to get complete lists • Examples for compound searching:

  19. Search Genes/Proteins/RNAs • List All buttons – quick way to get complete lists • Extensive filtering options

  20. Search Pathways

  21. Advanced Search • The BioVelo query language • SAQP: Structured Advanced Query Page • Permits the definition of complex searches without mastering BioVelo. To learn more about the advanced query interface, see online documentation.

  22. Sequence Search by BLAST • Nothing unusual here – a regular BLAST interface that permits BLASTing sequences against BioCyc PGDBs. • The results are linked to the PGDB gene/protein pages

  23. Growth Media and Phenotype • The desktop version of Pathway Tools allows definition of growth media, gene knockout growth information, and growth data for phenotype microarray plates.

  24. EcoCyc-Specific Searches: Growth Media Search for growth media based on: • name • compounds present • compounds not present • observed growth

  25. EcoCyc-Specific Searches: Textpresso • Mining E. coli literature poses special challenges – because almost every molecular biology paper references E. coli • The solution – EcoCyc Textpresso! An E. coli only collection of literature • 30,000 full-text articles and 6,500 abstracts. • Full text literature searches • Results presented at bottom of page

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